The Heating Ventilation and Air Conditioning (HVAC) systems are essential loads in world energy consumption. The proper management of these loads produces a reduction in energy demand. Colombia is an agricultural country, one of its favorite products is flowers. That product needs to be refrigerated for three months to maintain its quality or complete many flowers (a batch) to export and commercialize. In favor of this reason, it is crucial to have an exemplary refrigeration system or improve the current one. This article presents the comparison among some standard system identification algorithms. This development is vital to the flower greenhouses in the Boyacá region to improving efficiency in the post-harvest stage. Matlab software makes the data processing and executes some system identification algorithms in order to determine the most suitable tool for flower greenhouse cooling systems. This process aims to get a fitting percentage above 80%. As a result, the N4SID algorithm presents the best performance with a fitting of 81.23%.